Wrapping Up Hydrophobic Hydration: Locality Matters.

Water, being the universal solvent, acts as a competing agent in fundamental processes, such as folding, aggregation or biomolecular recognition. A molecular understanding of hydrophobic hydration is of central importance to understanding the subtle free energy differences, which dictate function. Ab initio and classical molecular dynamics simulations yield two distinct hydration water populations in the hydration shell of solvated tert-butanol noted as "HB-wrap" and "HB-hydration2bulk". The experimentally observed hydration water spectrum can be dissected into two modes, centered at 164 and 195 cm-1. By comparison to the simulations, these two bands are attributed to the "HB-wrap" and "HB-hydration2bulk" populations, respectively. We derive a quantitative correlation between the population in each of these two local water coordination motifs and the temperature dependence of the solvation entropy. The crossover from entropy to enthalpy dominated solvation at elevated temperatures, as predicted by theory and observed experimentally, can be rationalized in terms of the distinct temperature stability and thermodynamic signatures of "HB-wrap" and "HB-hydration2bulk".

Polymorphism of human telomeric quadruplexes with drugs: a multi-technique biophysical study.

The human telomeric G-quadruplex structural motif of DNA has come to be known as a new and stimulating target for anticancer drug discovery. Small molecules that interact with G-quadruplex structures in a selective way have gained impressive interest in recent years as they may serve as potential therapeutic agents. Here, we show how circular dichroism, UV resonance Raman and small angle X-ray scattering spectroscopies can be effectively combined to provide insights into structural and molecular aspects of the interaction between human telomeric quadruplexes and ligands. This study focuses on the ability of berberine and palmatine to bind with human telomeric quadruplexes and provides analysis of the conformational landscape visited by the relevant complexes upon thermal unfolding. With increasing temperature, both free and bound G-quadruplexes undergo melting through a multi-state process, populating different intermediate states. Despite the structural similarity of the two ligands, valuable distinctive features characterising their interaction with the G-quadruplex emerged from our multi-technique approach.

Identification of Pistacia-associated flexivirus 1, a putative mycovirus of the family Gammaflexiviridae, in the mastic tree (Pistacia lentiscus) transcriptome.

In this study, we identified the genome sequence of the novel virus Pistacia-associated flexivirus 1 (PAFV1), a putative member of the mycovirus family Gammaflexiviridae (the order Tymovirales), via analysis of a transcriptome dataset for the mastic tree (Pistacia lentiscus, the family Anacardiaceae). PAFV1 was predicted to have three open reading frames (ORFs): ORF1, encoding a replicase (REP) with RNA-dependent RNA polymerase activity; ORF2, a movement protein (MP); and ORF3, a hypothetical protein. The PAFV1 REP sequence showed high similarity to those of three known members of the family Gammaflexiviridae i.e., Entoleuca gammaflexivirus 1 (EnFV1), Entoleuca gammaflexivirus 2 (EnFV2), and Botrytis virus F (BVF). A genome contig of the fungus Monosporascus cannonballus also contained a sequence of an endogenous virus similar to that of PAFV1. Sequence comparison and phylogenetic analysis indicated that PAFV1, EnFV1, and the endogenous virus of M. cannonballus formed a distinct subgroup (apart from EnFV2 and BVF), and may be the founding members of a novel genus in the family Gammaflexiviridae. Notably, MP sequences of PAFV1/EnFV1 showed similarity to the MP sequences of the mycovirus group called tobamo-like mycoviruses (an unassigned taxon), implying that genomic recombination occurred between members of the family Gammaflexiviridae and tobamo-like mycoviruses. Since PAFV1 is phylogenetically related to mycoviruses, PAFV1 may also be a mycovirus that infected a fungus associated with the mastic tree sample, which is evidenced by the presence of fungal ribosomal RNA sequences in the mastic tree transcriptome. Thus, the PAFV1 genome sequence may be useful in elucidating the genome evolution of Gammaflexiviridae and tobamo-like mycoviruses. Keywords: Pistacia-associated flexivirus 1; Gammaflexiviridae; mycovirus, mastic tree.

Novel Divavirus (the family Betaflexiviridae) and Mitovirus (the family Narnaviridae) species identified in basil (Ocimum basilicum).

Transcriptome data obtained from a plant sample often contain a large number of reads that are derived from associated RNA virus genomes that were co-isolated during RNA preparation. These virus-derived reads can be assembled into a novel plant RNA genome sequence. Here, a basil (Ocimum basilicum) transcriptome dataset was analyzed to identify two new RNA viruses, which were named Ocimum basilicum RNA virus 1 (ObRV1) and Ocimum basilicum RNA virus 2 (ObRV2). A phylogenetic analysis of the ObRV1 RNA-dependent RNA polymerase (RdRp) motif indicated that ObRV1 is a novel species of the genus Divavirus of the family Betaflexiviridae. ObRV1 is the fourth divavirus species to be identified. The ObRV2 RdRp motif showed sequence similarity to viruses of the genus Mitovirus of the family Narnaviridae, which infect fungal mitochondria. Although most of the known mitoviruses do not produce a functional RdRp using the plant mitochondrial genetic code, the ObRV2 encodes a full-length RdRp using both the fungal and plant mitochondrial genetic codes.

Identification of a novel plant amalgavirus (Amalgavirus, Amalgaviridae) genome sequence in Cistus incanus.

Amalgaviridae is a family of double-stranded, monosegmented RNA viruses that are associated with plants, fungi, microsporidians, and animals. A sequence contig derived from the transcriptome of a eudicot, Cistus incanus (the family Cistaceae; commonly known as hoary rockrose), was identified as the genome sequence of a novel plant RNA virus and named Cistus incanus RNA virus 1 (CiRV1). Sequence comparison and phylogenetic analysis indicated that CiRV1 is a novel species of the genus Amalgavirus in the family Amalgaviridae. The CiRV1 genome contig has two overlapping open reading frames (ORFs). ORF1 encodes a putative replication factory matrix-like protein, while ORF2 encodes a RNA-dependent RNA polymerase (RdRp) domain. An ORF1+2 fusion protein, which functions in viral RNA replication, is produced by a +1 programmed ribosomal frameshifting (PRF) mechanism. A +1 PRF motif UUU_CGU, which matches the conserved amalgavirus +1 PRF consensus sequence UUU_CGN, was found at the boundary of CiRV1 ORF1 and ORF2. Comparison of 25 amalgavirus ORF1+2 fusion proteins revealed that only three different positions within a 13-amino acid segment were recurrently used at the boundary, possibly being selected so as not to interfere with correct folding and function of the fusion protein. CiRV1 is the first virus found to be associated with the Cistus species and may be useful for studying amalgaviruses.

Hydration-dependent dynamics of human telomeric oligonucleotides in the picosecond timescale: a neutron scattering study.

The dynamics of the human oligonucleotide AG3(T2AG3)3 has been investigated by incoherent neutron scattering in the sub-nanosecond timescale. A hydration-dependent dynamical activation of thermal fluctuations in weakly hydrated samples was found, similar to that of protein powders. The amplitudes of such thermal fluctuations were evaluated in two different exchanged wave-vector ranges, so as to single out the different contributions from intra- and inter-nucleotide dynamics. The activation energy was calculated from the temperature-dependent characteristic times of the corresponding dynamical processes. The trends of both amplitudes and activation energies support a picture where oligonucleotides possess a larger conformational flexibility than long DNA sequences. This additional flexibility, which likely results from a significant relative chain-end contribution to the average chain dynamics, could be related to the strong structural polymorphism of the investigated oligonucleotides.

Terahertz Dynamics in Human Cells and Their Chromatin.

The terahertz dynamics of human cells of the U937 line and their chromatin has been investigated by high-resolution inelastic X-ray scattering. To highlight its dynamical features in situ, nuclear DNA has been stained by uranyl-acetate salt. The general behavior of the collective dynamics of the whole cell is quite similar to that of bulk water, with a nearly wavevector-independent branch located at about 5 meV and a propagating mode with a linear trend corresponding to a speed of sound of 2900 ± 100 m/s. We provide the first experimental evidence for the existence of two branches also in the dispersion curves of chromatin. The high-energy mode displays an acoustic-like behavior with a sound velocity similar to unstained cells, but in this case the branch likely originates from the superposition of intramolecular DNA optic modes. A low-energy optic-like branch, distinctive of the chromatin moiety, is found at about 2.5 meV.

Membrane thickness and the mechanism of action of the short peptaibol trichogin GA IV.

Trichogin GA IV (GAIV) is an antimicrobial peptide of the peptaibol family, like the extensively studied alamethicin (Alm). GAIV acts by perturbing membrane permeability. Previous data have shown that pore formation is related to GAIV aggregation and insertion in the hydrophobic core of the membrane. This behavior is similar to that of Alm and in agreement with a barrel-stave mechanism, in which transmembrane oriented peptides aggregate to form a channel. However, while the 19-amino acid long Alm has a length comparable to the membrane thickness, GAIV comprises only 10 amino acids, and its helix is about half the normal bilayer thickness. Here, we report the results of neutron reflectivity measurements, showing that GAIV inserts in the hydrophobic region of the membrane, causing a significant thinning of the bilayer. Molecular dynamics simulations of GAIV/membrane systems were also performed. For these studies we developed a novel approach for constructing the initial configuration, by embedding the short peptide in the hydrophobic core of the bilayer. These calculations indicated that in the transmembrane orientation GAIV interacts strongly with the polar phospholipid headgroups, drawing them towards its N- and C-termini, inducing membrane thinning and becoming able to span the bilayer. Finally, vesicle leakage experiments demonstrated that GAIV activity is significantly higher with thinner membranes, becoming similar to that of Alm when the bilayer thickness is comparable to its size. Overall, these data indicate that a barrel-stave mechanism of pore formation might be possible for GAIV and for similarly short peptaibols despite their relatively small size.

Nuclear microsatellites for Pinus pinea (Pinaceae), a genetically depauperate tree, and their transferability to P. halepensis.

PREMISE OF THE STUDY: Pinus pinea is one of the few widespread plant species that are also genetically depauperate. It is also an important commercial species with high market value seeds. A deeper knowledge of the existing population genetic variation was needed. METHODS AND RESULTS: Twelve nuclear microsatellites were isolated from genomic and cDNA sequences and screened for variability in 729 individuals from 33 natural populations. Low level of genetic variability was confirmed with average expected heterozygosity of 0.11. Hardy-Weinberg equilibrium expectations were not met in only ∼10% of the possible locus/population combinations. All loci were in linkage equilibrium, and the frequency of null alleles was very low (≤1% in 332 out of 396 locus/population combinations). Nine out of the 12 microsatellites were successfully transferred to P. halepensis. CONCLUSIONS: Despite low polymorphism, these new markers will be useful to resolve population structure and hold potential for seed origin identification and traceability.

Water dynamics as affected by interaction with biomolecules and change of thermodynamic state: a neutron scattering study.

The dynamics of water as subtly perturbed by both the interaction with biomolecules and the variation of temperature and pressure has been investigated via neutron scattering spectroscopy. A measurement of inelastic neutron scattering devoted to the study of the coherent THz dynamics of water in a water-rich mixture with DNA (hydration level of 1 g DNA/15 g D(2)O) at room temperature is reported. The DNA hydration water coherent dynamics is characterised by the presence of collective modes, whose dispersion relations are similar to those observed in bulk water. These dispersion relations are well described by the interaction model developed in the case of bulk water, and the existence of a fast sound is experimentally demonstrated. The behaviour of the collective water dynamics was complemented by studying the single-particle dynamics of bulk water along the isotherm T = 298 K in the pressure range 0.1-350 MPa by means of incoherent scattering. This experiment is an attempt to simulate the change of the water molecular arrangement due to the interaction with DNA, by increasing the pressure as the presence of the biomolecule produces an increase in the density. An anomaly is found in the behaviour of the relaxation time derived from the quasi-elastic scattering signal, which can be related to the hypothetical second critical point in water. This anomaly and the transition from slow to fast sound take place in the same Q range, thus suggesting that the two phenomena could be related at some microscopic level.

Transcriptome changes in the cambial region of poplar (Populus alba L.) in response to water deficit.

A transcriptome analysis of the Populus alba cambial region was performed with the aim of elucidating the gene network underlying the response to water deficit within the cambium and differentiating derivative cambial cells. Water stress was induced in 1-year-old P. alba plants by withholding water for 9 days. At that time, leaf predawn water potential fell to -0.8 MPa, resulting in a significant reduction in stomatal conductance, CO(2) assimilation and a consistent increment of stem shrinkage. These effects were almost fully reversed by re-hydration. The water deficit resulted in changes in gene expression that affected several functional categories, such as protein metabolism, cell wall metabolism, stress response, transporters and transcriptional regulation. The function of up- and down-regulated genes is discussed considering the physiological response of the plants to water deficit.

Spatial genetic structure of Taxus baccata L. in the western Mediterranean Basin: past and present limits to gene movement over a broad geographic scale.

English yew (Taxus baccata L., Taxaceae), a Tertiary relict, provides a seminal example of a widespread albeit locally endangered (often close to extinction) tree species. In order to gain detailed insights into the evolutionary dynamics of the species on a broad geographical scale, over 1000 trees from 91 populations of English yew in the western Mediterranean were analyzed using seven nuclear microsatellite markers. Our results revealed contrasting patterns of genetic structure at different spatial scales: genetic variation was highly structured at the local scale, while only a low proportion of the observed variation was attributed to regional differences. We also found a geographic gradient of decreasing diversity and increasing population divergence from northwest (central Europe and northern Iberian Peninsula) to southeast (Mediterranean Iberia and North Africa). The patterns revealed in this study probably reflect the combined effects of Quaternary climatic changes and recent impact of human activities, and potentially also more ancient events dating back to the Tertiary. Both climatic and anthropogenic factors seem to have conducted to a long history of population isolation, which may have contributed significantly to enhance population divergence through restricted gene flow and genetic drift.

Is Cupressus sempervirens native in Italy? An answer from genetic and palaeobotanical data.

This study represents the first large-scale analysis using nuclear molecular markers to assess genetic diversity and structure of Cupressus sempervirens L.. Genetic and fossil data were combined to infer the possible role of human activity and evolutionary history in shaping the diversity of cypress populations. We analysed 30 populations with six polymorphic nuclear microsatellite markers. Dramatic reductions in heterozygosity and allelic richness were observed from east to west across the species range. Structure analysis assigned individuals to two main groups separating central Mediterranean and eastern populations. The two main groups could be further divided into five subgroups which showed the following geographical distributions: Turkey with the Greek islands Rhodes and Samos, Greece (Crete), Southern Italy, Northern Italy, Tunisia with Central Italy. This pattern of genetic structure is also supported by SAMOVA and Barrier analyses. Palaeobotanical data indicated that Cupressus was present in Italy in the Pliocene, Pleistocene and Holocene. Furthermore, our molecular survey showed that Italian cypress populations experienced bottlenecks that resulted in reduced genetic diversity and allelic richness and greater genetic differentiation. Recent colonization or introduction may also have influenced levels of diversity detected in the Italian populations, as most individuals found in this range today have multilocus genotypes that are also present in the eastern range of the species. The data reveal a new interpretation of the history of cypress distribution characterized by ancient eastern populations (Turkey and Greek islands) and a mosaic of recently introduced trees and remnants of ancient, depauperate populations in the central Mediterranean range.

Isolation and characterization of polymorphic nuclear microsatellite loci in Pinus cembra L.

We developed eight polymorphic nuclear microsatellite markers for the Swiss stone pine (Pinus cembra L.), of which seven may be amplified in a multiplex polymerase chain reaction. Allelic polymorphism across all loci and 40 individuals representing two populations in the Swiss Alps was high (mean = 7.6 alleles). No significant linkage disequlibrium was displayed between pairs of loci. Significant deviation from Hardy-Weinberg equilibrium was revealed at three loci in one population. Cross-amplification was achieved in two related species within the genus (P. sibirica and P. pumila). Thus, the markers may be useful for population genetic studies in these three pine species. They will be applied in ongoing projects on genetic diversity and patterns of gene flow in P. cembra.

Development and characterization of eight polymorphic microsatellite loci from Pistacia lentiscus L. (Anacardiaceae).

We have developed a set of eight polymorphic nuclear microsatellite markers for the Mediterranean shrub Pistacia lentiscus by means of an enriched library method. Characterization for the eight loci was carried out on 42 individuals from two populations sampled in southern Spain. The overall number of alleles detected was 59, ranging from three to 13 per locus. Expected heterozygosity per locus and population ranged from 0.139 to 0.895. Two loci albeit only in one population (Seville) departed significantly from Hardy-Weinberg equilibrium expectations and no linkage disequilibrium between pairs of loci was detected. These markers will be used in studies of gene flow across a fragmented landscape.

The distribution of Quercus suber chloroplast haplotypes matches the palaeogeographical history of the western Mediterranean.

Combining molecular analyses with geological and palaeontological data may reveal timing and modes for the divergence of lineages within species. The Mediterranean Basin is particularly appropriate for this kind of multidisciplinary studies, because of its complex geological history and biological diversity. Here, we investigated chloroplast DNA of Quercus suber populations in order to detect possible relationships between their geographical distribution and the palaeogeographical history of the western Mediterranean domain. We analysed 110 cork oak populations, covering the whole distribution range of the species, by 14 chloroplast microsatellite markers, among which eight displayed variation among populations. We identified five haplotypes whose distribution is clearly geographically structured. Results demonstrated that cork oak populations have undergone a genetic drift geographically consistent with the Oligocene and Miocene break-up events of the European-Iberian continental margin and suggested that they have persisted in a number of separate microplates, currently found in Tunisia, Sardinia, Corsica, and Provence, without detectable chloroplast DNA modifications for a time span of over 15 million years. A similar distribution pattern of mitochondrial DNA of Pinus pinaster supports the hypothesis of such long-term persistence, in spite of Quaternary climate oscillations and of isolation due to insularity, and suggests that part of the modern geographical structure of Mediterranean populations may be traced back to the Tertiary history of taxa.

Chloroplast DNA phylogeography of European ashes, Fraxinus sp. (Oleaceae): roles of hybridization and life history traits.

We investigated range-wide phylogeographic variation in three European ash species (Fraxinus sp., Oleaceae). Chloroplast DNA (cpDNA) microsatellites were typed in the thermophilous Fraxinus angustifolia and Fraxinus ornus and the observed haplotypes and the geographic distribution of diversity were compared to cpDNA data previously obtained in the more cold-tolerant Fraxinus excelsior. We found wide-ranging haplotype sharing between the phylogenetically close F. angustifolia and F. excelsior, suggesting hybridization (i) in common glacial refuges in the Iberian Peninsula, northern Italy, the eastern and/or Dinaric Alps and the Balkan Peninsula, and/or (ii) during postglacial recolonization. The data allowed us to propose additional glacial refuges for F. angustifolia in southern Italy and in Turkey, and populations from the latter region were particularly polymorphic. There was evidence for refuge areas in Italy, the Balkan Peninsula and Turkey for F. ornus, which did not share any single chloroplast haplotype with the other species. In both F. angustifolia and F. ornus, cpDNA diversity (h(S) = 0.027 and h(S) = 0.009, respectively) was lower and fixation levels (G(ST) = 0.964 and G(ST) = 0.983, respectively) higher than in sympatric F. excelsior (h(S) = 0.096, G(ST) = 0.870). These diversity patterns could be due to temperature tolerance or the demographic history.

Molecular differentiation of the Old World Culicoides imicola species complex (Diptera, Ceratopogonidae), inferred using random amplified polymorphic DNA markers.

Samples of seven of the 10 morphological species of midges of the Culicoides imicola complex were considered. The importance of this species complex is connected to its vectorial capacity for African horse sickness virus (AHSV) and bluetongue virus (BTV). Consequently, the risk of transmission may vary dramatically, depending upon the particular cryptic species present in a given area. The species complex is confined to the Old World and our samples were collected in Southern Africa, Madagascar and the Ivory Coast. Genomic DNA of 350 randomly sampled individual midges from 19 populations was amplified using four 20-mer primers by the random amplified polymorphic DNA (RAPD) technique. One hundred and ninety-six interpretable polymorphic bands were obtained. Species-specific RAPD profiles were defined and for five species diagnostic RAPD fragments were identified. A high degree of polymorphism was detected in the species complex, most of which was observed within populations (from 64 to 76%). Principal coordinate analysis (PCO) and cluster analysis provided an estimate of the degree of variation between and within populations and species. There was substantial concordance between the taxonomies derived from morphological and molecular data. The amount and the different distributions of genetic (RAPD) variation among the taxa can be associated to their life histories, i.e. the abundance and distribution of the larval breeding sites and their seasonality.